I got this via email from Patrick Woolsey, Director of Technical Services at BareBones Software:

BBEdit does indeed include preferences which allow you to change the behavior of Command- and Option-arrow key combinations, among other behaviors.

These options can be set in the Text Editing panel of BBEdit's Prefs window (see Chapter 10 of the user manual), while the "Cursor Movement and Text Selection" section in Chapter 4 covers what you might expect from its name :-), and Appendix B summarizes the available mouse and keyboard text selection and deletion commands.